interactive molecular dynamics (imd)
DESCRIPTION
Interactive Molecular Dynamics (IMD). IMD allows the user to guide and receive feedback from a running simulation Our demo illustrates IMD using the following components Visualization program (VMD, UIUC) Simulation program (ProtoMol, Notre Dame) IMD API (UIUC/Notre Dame) - PowerPoint PPT PresentationTRANSCRIPT
Presentation-SC2001
Interactive Molecular Dynamics (IMD)
• IMD allows the user to guide and receive feedback from a running simulation
• Our demo illustrates IMD using the following components– Visualization program (VMD, UIUC)– Simulation program (ProtoMol, Notre
Dame)– IMD API (UIUC/Notre Dame)– Haptic Device (Phantom, Sensable
Technologies)– Web based collaboratory for sharing
applications and data (BioCoRE, UIUC, www.ks.uiuc.edu/Research/biocore/)
ProtoMol (simulation)
VMD (visualization)
IMD
BioCoRE (web services)
Presentation-SC2001
Interactive Simulation Interfaces
OBJECTIVE: Interactive interfaces for ProtoMol
• User friendly interface to setup, monitor, and steer simulations
• Ability to quickly experiment with molecules and cells
APPROACH:• 3-D Visualization using OpenGL• Sockets interface between ProtoMol
and visualization component• Haptic Device interface• Availability over the web through a
generic GUI (BioCoRE, http://www.ks.uiuc.edu/Research/biocore/)
Presentation-SC2001
ProtoMol
OBJECTIVE: Make ProtoMol a more scalable parallel program
• Hundreds of nodes
• Heterogeneous platforms APPROACH:• Abstract parallel layer
• Dynamic load balancing
• Multithreading
• More scalable algorithms
• Future availability of ProtoMol simulations over web (thru’ BioCoRE)
ProtoMol--parallel software framework for the simulation of bio-molecules
ProtoMol is open source and available at http://www.cse.nd.edu/~lcls/Protomol.html
Presentation-SC2001
• VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies.
• VMD is available at: http://www.ks.uiuc.edu/Research/vmd
• VMD is already available as an application and data sharing model for web based collaboratory research at BioCoRE (http://www.ks.uiuc.edu/Research/biocore/)
VMD